Novel green algal isolates from the Egyptian hyper‐arid desert oases: a polyphasic approach with a description of Pharao desertorum gen. et sp. nov. (Chlorophyceae,Chlorophyta)

The biodiversity of terrestrial algae is still grossly understudied, and African deserts in particular are barely touched in this respect. Here, four coccoid green algae from oases in the Western Desert of Egypt were characterized using a combination of morphotaxonomic, ecological and 18S rDNA data, with additional carotenoid and lipid analyses for two of the strains. Three strains were identified as affiliated with known taxa: Mychonastes sp., Asterarcys sp. (first report of this genus from a desert soil), and Stichococcus cf. deasonii. The fourth strain is proposed to represent a new cryptic genus Pharao gen. nov., with the type species P. desertorum sp. nov. The new taxon is sister to the clade of uncharacterized North American desert strains of Radiococcaceae (Chlorophyceae, Chlorophyta). The pigment profile of P. desertorum gen. et sp. nov. revealed carotenoids and chlorophylls typical of green algae. Bioorganic analysis showed a complex lipidome based on phospho‐ (PC), galacto‐ (MGDG and DGDG), betaine‐ (DGTS), and sulfoquinovosyl‐ (SQDG) membrane lipids, besides significant amounts of storage neutral lipids such as diacyl‐ (DAG) and triacylglycerols (TAG). The presence of saturated alkyl chains within all the membrane lipid classes in P. desertorum and Asterarcys sp. appears to reflect the need to maintain membrane fluidity and viscosity. In summary, African deserts likely still harbor new taxa to be described, and lipidomic analyses of such taxa may provide clues about their ability to survive in the extremely harsh desert habitats.     

Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin Sandy Land,northeast China

Caragana microphylla (Leguminosae) is a dominant climax semishrub species in northern China. We evaluated genetic variation within and among populations sampled from three different environmental gradients in Horqin Sandy Land in northern China using intersimple sequence repeats markers and investigated the possible existence of relationships between genetic diversity and environmental factors. The results showed that C. microphylla have high genetic diversity, and environmental gradients affected genetic diversity of C. microphylla populations. Genetic diversity of all populations was affected by many environmental factors and as well correlated with warm index and soil Olsen phosphorus (SOP) concentration. These results have important implications for restoration and management of these degraded ecosystems in arid and semi‐arid areas.     

Species differentiation and gene flow in the Blackbutts (genus <Emphasis Type="Italic">Eucalyptus</Emphasis> subgenus <Emphasis Type="Italic">Eucalyptus</Emphasis> section <Emphasis Type="Italic">Pseudophloius</Emphasis>)

The significance of the taxonomic distinction of two species of Blackbutt was studied by analysing patterns of genetic (microsatellite markers; n = 13) and phenetic (capsule morphology) differentiation. Analysis of genetic structure using a Bayesian modelling approach on range-wide samples of both taxa (n = 457) showed the major division was within the more widely distributed species, Eucalyptus pilularis, and not aligned with taxonomy. Comparisons of intra- and inter-taxon genetic differentiation in paired-samples of taxa from each of four locations spanning the distribution of the more restricted E. pyrocarpa, showed that around twice as much variation was found among locations within taxa, than between taxa. Despite the lack of differentiation at effectively neutral microsatellite markers, significant phenetic differences (including capsule size) were evident between taxa at most sites. A landscape mosaic of taxa, coincident with changes in elevation, vegetation and soil types, suggested some phenetic differences were probably adaptive and spatial differentiation was stabilised by environmental factors. An absence of morphological intermediates and a lack of correlation in the rankings of locus inter-taxon differentiation (Phi_BT) across locations, was consistent with parapatric origins for E. pyrocarpa. We conclude the taxa are at the lower end of the speciation spectrum and might best be viewed as ecotypes, divergent in evolutionary potential, but with genomes broadly permeable to inter-taxa gene flow. Gene exchange between plantings of E. pilularis and nearby E. pyrocarpa forest is likely as the two taxa appear to have few barriers to reproduction.     

Genetic differentiation,hybridization and adaptive divergence in two subspecies of the acorn barnacle Tetraclita japonica in the northwestern Pacific

Two acorn barnacles, Tetraclita japonica japonica and Tetraclita japonica formosana, have been recently reclassified as two subspecies, because they are morphologically similar and genetically indistinguishable in mitochondrial DNA sequences. The two barnacles are distinguishable by parietes colour and exhibit parapatric distributions, coexisting in Japan, where T. j. formosana is very low in abundance. Here we investigated the genetic differentiation between the subspecies using 209 polymorphic amplified fragment length polymorphism markers and 341 individuals from 12 locations. The subspecies are genetically highly differentiated (Φ_CT = 0.267). Bayesian analysis and principal component analysis indicate the presence of hybrids in T. j. formosana samples from Japan. Strong differentiation between the northern and southern populations of T. j. japonica was revealed, and a break between Taiwan and Okinawa was also found in T. j. formosana. The differentiation between the two taxa at individual loci does not deviate from neutral expectation, suggesting that the oceanographic pattern which restricts larval dispersal is a more important factor than divergent selection in maintaining genetic and phenotypic differentiation. The T. j. formosana in Japan are probably recent migrants from Okinawa, and their presence in Japan may represent a poleward range shift driven by global warming. This promotes hybridization and might lead to a breakdown of the boundary between the subspecies. However, both local adaptation and larval dispersal are crucial in determining the population structure within each subspecies. Our study provides new insights into the interplay of local adaptation and dispersal in determining the distribution and genetic structure of intertidal biota and the biogeography of the northwestern Pacific.     

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among‐species differentiation accounts for 35% of the total genetic differentiation (F_ST = 0.35), and F_ST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.     

Northern genetic richness and southern purity,but just one species in the Chelonoidis chilensis complex

Fritz, U., Alcalde, L., Vargas‐Ramírez, M., Goode, E.V., Fabius‐Turoblin, D.U. & Praschag, P. (2012). Northern genetic richness and southern purity, but just one species in the Chelonoidis chilensis complex. —Zoologica Scripta, 41, 220–232. The Chelonoidis chilensis complex, the sister group of the famous Galápagos tortoises, is a widely distributed group of South American land tortoises, ranging from the dry Chaco of Bolivia, Paraguay and northern Argentina to northern Patagonia. Within this complex, up to three distinct species have been recognized. Using sequence data of the mitochondrial cytochrome b gene and length polymorphisms of 10 microsatellite loci, we investigate genetic differentiation among all three nominal species. We find only negligible differentiation, with decreasing genetic diversity from north to south. We conclude that only one species, Chelonoidis chilensis (Gray, 1870), is valid, with C. donosobarrosi ( Freiberg, 1973 ) and C. petersi ( Freiberg, 1973 ) as its junior synonyms. Morphological variation within C. chilensis sensu lato is in accord with the observation that size variation in chelonians follows Bergmann’s rule, with body size increasing with latitude. The observed phylogeographic differentiation inverses the well‐known pattern of southern genetic richness and northern purity from the northern hemisphere, resulting from dispersal from glacial refugia. This implies that in higher latitudes of both hemispheres genetic diversity may decrease with increasing distance from the refugium. For C. chilensis sensu lato, it seems likely that long‐distance dispersal via rafting on the Desaguadero River led to the foundation of the southernmost populations in northern Patagonia during the Holocene.     

Evidence that Kenyan House Sparrows Passer domesticus invaded from multiple sites

Here we characterize genetic patterns across the range of House Sparrows in Kenya using six microsatellite markers. We screened House Sparrows from two remote locations in northern Kenya, Marsabit (n = 24) and Wajir (n = 27), which are separated from other colonized areas in Kenya by minimally developed, arid habitat, and then compared these birds with House Sparrows in 10 more central and longer established Kenyan cities (n = 233) in this range. House Sparrows from Marsabit and Wajir originated from a separate source, probably Somalia and/or Ethiopia, from other Kenyan House Sparrows, probably Mombasa. Furthermore, the genetic characteristics of northern and southern populations indicate that they have not yet mixed, supporting a hypothesis that the large, minimally (human) developed, arid landscape spanning nearly all of northern Kenya, including the 100 000 km² Chalbi Desert, is a barrier to dispersal for House Sparrows.     

Low genetic variation of invasive Fallopia spp. in their northernmost European distribution range

Knowledge about the reproduction strategies of invasive species is fundamental for effective control. The invasive Fallopia taxa (Japanese knotweed s.l.) reproduce mainly clonally in Europe, and preventing spread of vegetative fragments is the most important control measure. However, high levels of genetic variation within the hybrid F. × bohemica indicate that hybridization and seed dispersal could be important. In Norway in northern Europe, it is assumed that these taxa do not reproduce sexually due to low temperatures in the autumn when the plants are flowering. The main objective of this study was to examine the genetic variation of invasive Fallopia taxa in selected areas in Norway in order to evaluate whether the taxa may reproduce by seeds in their most northerly distribution range in Europe. Fallopia stands from different localities in Norway were analyzed with respect to prevalence of taxa, and genetic variation within and between taxa was studied using amplified fragment length polymorphism (AFLP). Taxonomic identification based on morphology corresponded with identification based on simple sequence repeats (SSR) and DNA ploidy levels (8× F. japonica, 6× F. × bohemica and 4× F. sachalinensis). No genetic variation within F. japonica was detected. All F. × bohemica samples belonged to a single AFLP genotype, but one sample had a different SSR genotype. Two SSR genotypes of F. sachalinensis were also detected. Extremely low genetic variation within the invasive Fallopia taxa indicates that these taxa do not reproduce sexually in the region, suggesting that control efforts can be focused on preventing clonal spread. Climate warming may increase sexual reproduction of invasive Fallopia taxa in northern regions. The hermaphrodite F. × bohemica is a potential pollen source for the male‐sterile parental species. Targeted eradication of the hybrid can therefore reduce the risk of increased sexual reproduction under future warmer climate.     

Environment and space as drivers of variation in skull shape in two widely distributed South‐American Tayassuidae,Pecari tajacu and Tayassu pecari (Mammalia: Cetartiodactyla)

The influence of the environment on the geographical variation of morphological traits has been recognized in a number of taxa. Pecari tajacu and Tayassu pecari are ideal models to investigate intraspecific geographic variation in skull because of their wide and heterogeneous geographical distribution in South America. We used geometric morphometric procedures to examine the geographical variation in skull shape of 294 adult specimens of these species from 134 localities. We quantified to what extent skull shape variation was explained by environment, skull size and geographical space using variation partitioning analysis. We detected a strong pattern of geographic variation for P. tajacu skull shape, but not for T. pecari. The environment seems to be the major selective force that drives skull shape variation in both species. Nevertheless, other spatially structured processes (e.g. genetic drift, gene flow) might also have affected variation in the skull shape of the more widespread species P. tajacu. Allometric relationships might reflect the biomechanical constraints that are thought to be strong enough to limit size‐related changes in T. pecari skull shape.     

Assessing the taxonomic status of Osmoderma cristinae (Coleoptera: Scarabaeidae), endemic to Sicily,by genetic,morphological and pheromonal analyses

Resolving complexes of closely related and cryptic insect species can be challenging, especially when dealing with rare and protected taxa that are difficult to collect for genetic and morphological analyses. Until recently, populations of the genus Osmoderma (Scarabaeidae), widespread in Europe, were treated as a single species O. eremita (Scopoli, 1763) in spite of observed geographic variation in morphology. A previous survey using sequence data from the mtDNA cytochrome C oxidase I gene (COI) revealed the occurrence of at least two distinct lineages within this species complex: O. eremita in the west and O. barnabita Motschulsky, 1845, in the east. Interestingly, beetles confined to Sicily have been described as a distinct species, O. cristinae Sparacio, 1994, based on morphological traits. Only few Sicilian specimens were included in the former genetic analysis, and the results led to a still questionable taxonomic rank for these populations. To explore the robustness of the previous taxonomic arrangement for O. cristinae, a combination of genetic, morphological and pheromonal analyses was used. A 617‐bp fragment of the COI gene, aligned with O. cristinae and O. eremita sequences already available in GenBank, showed a clear genetic divergence between the two species (interspecific mean distance = 6.6%). Moreover, results from AFLP markers sustained the distinction of the two species. In addition, geometric morphometric analyses of the shape of male genitalia revealed a clear differentiation between the two species. Via scent analysis and field trapping, we demonstrated the production of the sex pheromone (R)‐(+)‐γ‐decalactone by males of O. cristinae, the attraction by conspecific individuals (mostly females) to this compound, and a lack of antagonistic effect of (S)‐(–)‐γ‐decalactone. The fact that O. eremita and O. eremita use the same compound for mate finding suggests that this sex pheromone has not undergone a differentiation and probably the allopatry of these two species compensates for the absence of a mechanism to avoid cross‐attraction. Our genetic and morphological data support the divergence of the two species and confirm the species status for O. cristinae, while sex pheromones are confirmed to be invariant among different species of the genus Osmoderma.     

Combining geometric morphometrics,molecular phylogeny,and micropaleontology to assess evolutionary patterns in Mallomonas (Synurophyceae: Heterokontophyta)

Synurophytes, also known as scaled chrysophytes, are ecologically important algae that produce an array of siliceous structures upon which their taxonomy is based. Despite occupying a key position within the photosynthetic heterokonts, the evolutionary history of synurophytes remains poorly constrained. Here, modern and Middle Eocene siliceous scales of the morphotaxon Mallomonas insignis are used as a model to investigate synurophyte evolutionary patterns. Structural details of scale morphology were examined comparatively with scanning electron microscopy and scored for geometric morphometric analyses to assess the stability of shape characters. Although consistent size differences exist (modern scales are larger than Eocene counterparts), the populations cannot be differentiated on the basis of shape or microstructural detail, implying considerable evolutionary stasis in scale morphology. A time‐calibrated relaxed molecular clock analysis using a three‐gene concatenated data set (27 strains) suggests that the M. insignis lineage predates the available fossil record, having diverged from closest congeneric taxa in the Cretaceous (≥94 Ma). However, the molecular analysis also implies that considerable genetic variability is present within several morphotaxa of Mallomonas, implying that substantial genetic variability has arisen despite the retention of uniform scale morphologies, and resulting in the widespread occurrence of cryptic taxa. Results from the synurophyte lineage are consistent with the notion of protracted ghost ranges (>10 Ma) implied by the molecular phylogenies of other algal groups, together pointing to the paucity of the fossil record of these organisms on these timescales.     

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

Sponges are among the most species‐rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model‐based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single‐copy nuclear protein‐coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax, C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera, C. longissima, C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model‐based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.     

Phylogeography of the poison frog Mantella viridis (Amphibia: Mantellidae) reveals chromatic and genetic differentiation across ecotones in northern Madagascar

Mantella viridis is a threatened poison frog species endemic to the ecologically very heterogeneous northern region of Madagascar. The existence of several colour morphs within M. viridis and its very low genetic differentiation to the allopatrically distributed Mantella ebenaui raise questions about the processes driving the differentiation between these poison frog populations and about their taxonomic status. Using a DNA fragment of 476 nucleotides of the mitochondrial cytochrome b gene from 240 individuals of this species complex, we investigated the genetic variability of all known colour morphs of M. viridis, sampling this species throughout its known range, as well as several populations of M. ebenaui. Our genetic results confirm that M. viridis and M. ebenaui are closely related but reveal that no haplotype sharing occurs between these two taxa. Further, our molecular analyses provided evidence for barriers to gene flow among some of the colour morphs. Estimates of overlap of bioclimatic envelopes as assessed by ecological niche modelling also suggest a distinct bioclimatic niche of some of the lineages studied.     

Refugia,colonization and diversification of an arid‐adapted bird: coincident patterns between genetic data and ecological niche modelling

Phylogeographical studies are common in boreal and temperate species from the Palaearctic, but scarce in arid‐adapted species. We used nuclear and mitochondrial markers to investigate phylogeography and to estimate chronology of colonization events of the trumpeter finch Bucanetes githagineus, an arid‐adapted bird. We used 271 samples from 16 populations, most of which were fresh samples but including some museum specimens. Microsatellite data showed no clear grouping according to the sampling locations. Microsatellite and mitochondrial data showed the clearest differentiation between Maghreb and Canary Islands and between Maghreb and Western Sahara. Mitochondrial data suggest differentiation between different Maghreb populations and among Maghreb and Near East populations, between Iberian Peninsula and Canary Islands, as well as between Western Sahara and Maghreb. Our coalescence analyses indicate that the trumpeter finch colonized North Africa during the humid Marine Isotope Stage 5 (MIS5) period of the Sahara region 125 000 years ago. We constructed an ecological niche model (ENM) to estimate the geographical distribution of climatically suitable habitats for the trumpeter finch. We tested whether changes in the species range in relation to glacial–interglacial cycles could be responsible for observed patterns of genetic diversity and structure. Modelling results matched with those from genetic data as the species' potential range increases in interglacial scenarios (in the present climatic scenario and during MIS5) and decreases in glacial climates (during the last glacial maximum, LGM, 21 000 years ago). Our results suggest that the trumpeter finch responded to Pleistocene climatic changes by expanding and contracting its range.     

Molecular and plumage analyses indicate the incomplete separation of two woodpeckers (Aves,Picidae)

We evaluated the relationship between Celeus undatus and Celeus grammicus, with the objective of clarifying their evolutionary history. We analysed fragments of the mitochondrial and nuclear genes of 57 specimens. For comparative purposes, we inspected the plumage patterns of 77 skins. Our findings highlight the absence of reciprocal monophyly between the two taxa, given their reduced genetic divergence, and the lack of any clear separation of the two forms in the haplotype networks. A similar situation was found in the STRUCTURE analysis, with reciprocal contributions from the two taxa to the respective clusters, indicating that C. grammicus and C. undatus cannot be differentiated using the molecular markers. Corroborating the genetic data, our plumage analyses also failed to find any clear diagnostic characters between the polytypic C. undatus and C. grammicus, as they are defined at present. The genetic profile is consistent with either extensive historical gene flow between the species or, alternatively, incomplete lineage sorting, rather than recent secondary contact. The lack of monophyly between the two taxa impeded subspecies‐level phylogeographic inferences, with the subspecific variation being interpreted as a probable artefact of the phenotypic plasticity of the two forms. These findings indicate clearly that the two taxa form a single evolutionary unit, in which the morphological differentiation used to diagnose the species, combined with their geographic distribution, is at odds with the incomplete separation of the taxa. This may reflect disparities in the rates of differentiation between molecular and phenotypic markers, which is possibly due to the variation in selection pressures along a humidity gradient in Amazonia.     

Genetic rescue of an inbred captive population of the critically endangered Puerto Rican crested toad (<Emphasis Type="Italic">Peltophryne lemur</Emphasis>) by mixing lineages

The Puerto Rican crested toad (Peltophryne lemur) is currently composed of a single wild population on the south coast of Puerto Rico and two captive populations founded by animals from the northern and southern coasts. The main factors contributing to its decline are habitat loss, inundation of breeding ponds during storms, and impacts of invasive species. Recovery efforts have been extensive, involving captive breeding and reintroductions, habitat restoration, construction of breeding ponds, and public education. To guide future conservation efforts, genetic variation and differentiation were assessed for the two captive colonies and the remaining wild population using the mitochondrial control region and six novel microsatellite loci. Only two moderately divergent mitochondrial haplotypes were found, with one fixed in each of the southern and northern lineages. Moderate genetic variation exists for microsatellite loci in all three groups. The captive southern population has not diverged substantially from the wild population at microsatellite loci (F _ST = 0.03), whereas there is little allelic overlap between the northern and southern lineages at five of six loci (F _ST > 0.3). Despite this differentiation, they are no more divergent than many populations of other amphibian species. As the northern breeding colony may not remain viable due to its small size and inbred nature, it is recommended that a third breeding colony be established in which northern and southern individuals are combined. This will preserve any northern adaptive traits that may exist, and provide animals for release in the event that the pure northern lineage becomes extirpated.     

Late Quaternary climatic vegetational shifts in an ecological transition zone of northern Madagascar: insights from genetic analyses of two endemic rodent species

The Loky‐Manambato region, located in northern Madagascar, is a biotically rich contact zone between different forest biomes. Local current forest cover is composed of both humid and dry formations, which show elevational stratification. A recent phylogeographical study of a regional dry forest rodent, Eliurus carletoni (subfamily Nesomyinae), found genetic evidence of forest contractions between 18 750 and 7500 years BP, which based on extrapolation of the pollen subfossil record, was thought to be associated with an expansion of local humid forests. Herein, we conduct a genetic test of this hypothesis and focused on populations on two neighbouring massifs of forest‐dependent rodent species, one associated with low‐elevation dry forests (E. carletoni) and the other with higher elevation humid forests (Eliurus tanala). Using mitochondrial markers and a combination of traditional and coalescent‐based phylogeographical, historical demographic and population genetic methods, we found evidence of historical connections between populations of E. tanala. Adjacent populations of E. carletoni and E. tanala exhibit opposite historical demographic patterns, and for both, evidence suggests that historical demographic events occurred within the last 25 000 years BP. These findings strongly support the proposed late Quaternary shifts in the floristic composition of the Loky‐Manambato region.     

Conservation genetics of two island endemic Ribes spp. (Grossulariaceae) of Sardinia: survival or extinction?

Measuring levels of population genetic diversity is an important step for assessing the conservation status of rare or endangered plant species and implementing appropriate conservation strategies. Populations of Ribes multiflorum subsp. sandalioticum and R. sardoum, two endangered endemic species from Sardinia, representing the whole genus on the island, were investigated using ISSR and SSR markers to determine levels and structure of genetic variability in their natural populations. Results indicated medium to low genetic diversity at the population level: Nei's gene diversity for ISSR markers ranged from 0.0840 to 0.1316; the expected heterozygosity (H_E) for SSR ranged from 0.4281 to 0.7012. In addition, only one remnant population of R. sardoum showed a high level of inbreeding, in accordance with its very small size. Regarding the structure of the six R. sandalioticum populations, both principal coordinates analysis (PCoA) and STRUCTURE analysis of ISSR and SSR data highlighted low population structure, although two populations appeared to be clearly distinct from the others. The genetic pattern of the two taxa associated with their different ecological positions indicated resilience of R. sandalioticum populations in fresh and humid habitats and uncertain future resistance for the residual R. sardoum population in xeric calcareous stands. Hence, this study highlights the importance of an integrated conservation approach (genetic plus in situ and ex situ conservation studies/measures) for activating management programmes in these endemic and threatened taxa that can be considered as crop wild relatives of cultivated Ribes species.     

Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long‐lived tree endemic to Hainan Island,China

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long‐lived trees. Dracaena cambodiana is an endangered, long‐lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter‐simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat‐private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.